From: Georg Spiekermann (
Date: Mon Nov 30 2009 - 04:01:12 CST

Dear VMD community,

for visualization of silicate melts and glasses, the Polyhedra option
has this limitation: One cannot (yet) restrict the polyhedra around one
type of atom to be drawn just from ONE other neighbour type of atoms,
like oxygen in most cases.

Looking for a solution, I found this statement by Axel Kohlmeyer from
July 16th 2008 on VMD mailing list about the Polyhedra option:

"the one possible improvement that i am seeing (and i've been suggesting
something similar for dynamic bonds as well for quite a while now) would
be to have _two_ selections. one for the center and one for the
"neigbors". but i would expect that to matter only in very rare
cases, [...]"

Maybe someone has already made the small modification that would be
necessary for these two selections?

This would be useful for modellers that deal with silicate melts and
glasses that contain more atom types than just silicon and oxygen.

Kind regards,
Georg Spiekermann